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EPUBs with real page numbers are rare so few tools exist that work with them.
APNX files produced directly by calibre or by using the APNX plugin do not include pages defined in the NCX pageList, they only create approximately positioned pages based on a specified (or estimated) page count for the book.
Kindlegen will process a pageList and save it in the MOBI file produced, but I do not know of any software that can split out this information to produce a separate APNX file as needed for Kindle devices.
The KFX Output plugin for calibre will make use of an NCX pageList to produce KFX files containing real page numbers that can be sideloaded to Kindle devices. (KFX format does not rely on APNX files.)
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